How to get rid of fireflies coming from apartment windows?
I'm not sure that what you describe are fireflies but noise and pixelation resulting from rendering at a low resolution with low samples.

This is a render form your original file
just 100 samples at 50% resolution.
:

EDIT

Changing the glass of the windows to a node tree like this you can have transparency and reflections (look at the added emitter plane on the left).

Rendering with more samples at a higher resolution will give you a cleaner image.





For a deeper explanation on the nodes used please read this answer

Note the change with more samples and a higher resolution:



(click on the image to enlarge)